9OD0 | pdb_00009od0

Cryo-EM structure of the cytochrome bc complex (CIII2) from Bacillus subtilis with multiple Qi site menaquinone binding

PDB DOI: https://doi.org/10.2210/pdb9OD0/pdb
EM Map EMD-70337: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Bacillus subtilis
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2025-04-25 Released: 2026-11-04
Deposition Author(s): Gu, M., Zheng, W., Zong, Y., Zhang, K., Zhu, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the cytochrome bc complex (CIII2) from Bacillus subtilis with multiple Qi site menaquinone binding

Gu, M., Zheng, W., Zong, Y., Zhang, K., Zhu, J.

To be published.

Macromolecule Content

Total Structure Weight: 239.08 kDa
Atom Count: 16,398
Modeled Residue Count: 1,975
Deposited Residue Count: 2,000
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase iron-sulfur subunit	A, J [auth a]	167	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrA, bfcA, BSU22560
UniProt
Find proteins for P46911 (Bacillus subtilis (strain 168)) Explore P46911 Go to UniProtKB: P46911
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46911
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase cytochrome b subunit	B, K [auth b]	224	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrB, bfcB, BSU22550
UniProt
Find proteins for P46912 (Bacillus subtilis (strain 168)) Explore P46912 Go to UniProtKB: P46912
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46912
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase cytochrome c subunit	C, L [auth c]	255	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrC, bfcC, BSU22540
UniProt
Find proteins for P46913 (Bacillus subtilis (strain 168)) Explore P46913 Go to UniProtKB: P46913
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46913
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
YqgW	D, M [auth d]	57	Bacillus subtilis	Mutation(s): 0 Gene Names: yqgW, BSU24800
UniProt
Find proteins for P54500 (Bacillus subtilis (strain 168)) Explore P54500 Go to UniProtKB: P54500
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54500
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
YqgY	E, N [auth e]	81	Bacillus subtilis	Mutation(s): 0 Gene Names: yqgY, BSU24780
UniProt
Find proteins for P54502 (Bacillus subtilis (strain 168)) Explore P54502 Go to UniProtKB: P54502
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54502
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
QcrF	F, O [auth f]	23	Bacillus subtilis	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
QcrG	G, P [auth g]	29	Bacillus subtilis	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
YqzM	H, Q [auth h]	44	Bacillus subtilis	Mutation(s): 0 Gene Names: yqzM, BSU25569
UniProt
Find proteins for C0H453 (Bacillus subtilis (strain 168)) Explore C0H453 Go to UniProtKB: C0H453
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0H453
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
YlbA	I, R [auth i]	120	Bacillus subtilis	Mutation(s): 0 Gene Names: ylbA, BSU14940
UniProt
Find proteins for O34743 (Bacillus subtilis (strain 168)) Explore O34743 Go to UniProtKB: O34743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34743
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain JA [auth b] MOL2 format, chain JA [auth b] mmCIF format, chain JA [auth b]	JA [auth b]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain JA [auth b] Interactions & Density Focus chain JA [auth b]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] MOL2 format, chain CA [auth E] mmCIF format, chain CA [auth E]	CA [auth E]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain CA [auth E] Interactions & Density Focus chain CA [auth E]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain PA [auth e] SDF format, chain OA [auth c] SDF format, chain EA [auth a] SDF format, chain BA [auth C] MOL2 format, chain PA [auth e] MOL2 format, chain OA [auth c] MOL2 format, chain EA [auth a] MOL2 format, chain BA [auth C] mmCIF format, chain PA [auth e] mmCIF format, chain OA [auth c] mmCIF format, chain EA [auth a] mmCIF format, chain BA [auth C]	BA [auth C], EA [auth a], OA [auth c], PA [auth e]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain BA [auth C] Focus chain EA [auth a] Focus chain OA [auth c] Focus chain PA [auth e] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth a] Focus chain OA [auth c] Focus chain PA [auth e]
MQ7 Query on MQ7 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain MA [auth c] SDF format, chain LA [auth b] SDF format, chain KA [auth b] SDF format, chain IA [auth b] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain MA [auth c] MOL2 format, chain LA [auth b] MOL2 format, chain KA [auth b] MOL2 format, chain IA [auth b] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain MA [auth c] mmCIF format, chain LA [auth b] mmCIF format, chain KA [auth b] mmCIF format, chain IA [auth b]	IA [auth b] KA [auth b] LA [auth b] MA [auth c] W [auth B] IA [auth b], KA [auth b], LA [auth b], MA [auth c], W [auth B], X [auth B], Y [auth B], Z [auth B]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain IA [auth b] Focus chain KA [auth b] Focus chain LA [auth b] Focus chain MA [auth c] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth b] Focus chain KA [auth b] Focus chain LA [auth b] Focus chain MA [auth c] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain NA [auth c] SDF format, chain FA [auth b] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain NA [auth c] MOL2 format, chain FA [auth b] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain NA [auth c] mmCIF format, chain FA [auth b] mmCIF format, chain AA [auth C]	AA [auth C], FA [auth b], NA [auth c], T [auth B]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain AA [auth C] Focus chain FA [auth b] Focus chain NA [auth c] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth b] Focus chain NA [auth c] Focus chain T [auth B]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain HA [auth b] SDF format, chain GA [auth b] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain HA [auth b] MOL2 format, chain GA [auth b] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain HA [auth b] mmCIF format, chain GA [auth b]	GA [auth b], HA [auth b], U [auth B], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain GA [auth b] Focus chain HA [auth b] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain GA [auth b] Focus chain HA [auth b] Focus chain U [auth B] Focus chain V [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain DA [auth a] MOL2 format, chain S [auth A] MOL2 format, chain DA [auth a] mmCIF format, chain S [auth A] mmCIF format, chain DA [auth a]	DA [auth a], S [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DA [auth a] Focus chain S [auth A] Interactions & Density Focus chain DA [auth a] Focus chain S [auth A]